Bioinformatics. 2011 Apr 1;27(7):1011-2. Epub 2011 Jan 28.

SHRiMP2: sensitive yet practical SHort Read Mapping.

David M, Dzamba M, Lister D, Ilie L, Brudno M.

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Department of Computer Science, Princeton University, USA.

Abstract

We report on a major update (version 2) of the original SHort Read Mapping Program (SHRiMP). SHRiMP2 primarily targets mapping sensitivity, and is able to achieve high accuracy at a very reasonable speed. SHRiMP2 supports both letter space and color space (AB/SOLiD) reads, enables for direct alignment of paired reads and uses parallel computation to fully utilize multi-core architectures. AVAILABILITY: SHRiMP2 executables and source code are freely available at: http://compbio.cs.toronto.edu/shrimp/.

PMID:: 21278192; [PubMed - indexed for MEDLINE]

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